[phenixbb] Gap between R and Rfree

Pavel Afonine PAfonine at lbl.gov
Thu Feb 25 12:20:43 PST 2010

> General question: this topic comes up over and over again here and on ccp4bb.  Is there a general FAQ list anywhere that covers all of these issues?  (I will add this to the Phenix FAQ, along with the answer to "how do I tell if my R-free is good", but most of the same answers apply to any software, not just Phenix.)

The question "how do I tell if my R-free is good" that keeps coming up 
from time to time motivated us to write this paper:

Crystallographic model quality at a glance. L. Urzhumtseva, P. V. 
Afonine, P. D. Adams, A. Urzhumtsev Acta Cryst. D65, 297-300 (2009).

The corresponding tool, called POLYGON, is available in PHENIX. Related 
utility, "PDB Statistics Overview" is available in PHENIX as well.

So at this point we can automatically tell if the R-factors are good or 
not, and the next step in automation would be to take right refinement 
decisions based on this. Work in progress -:)


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